Why didn't I believe Greenwald initially? Well, I have had the dubious pleasure of seeing many people behave badly and then play the morally-outraged victim to try to legitimize it. There's a particular way they write and talk, and Greenwald's description of events reeked of it.
The Intercept's response made a few jabs but it didn't level any particular wild accusations, unlike Greenwald. It seemed much more credible, although clearly frustrated. I assume (reading between the lines) there he developed a prior history of conflicts and bad blood at the Intercept, and political differences. This kind of blow-up does not just come from nowhere.
The editors clearly had substantive journalistic concerns about the extent Greenwald was drawing conclusions from dubious evidence, and the lack of context around it. They're comfortable publishing the parts of the story he can substantiate, but not the parts that are weaker (or less on-topic). There have some political disagreements, but that's hardly censorship.
Why did you not believe the first side you heard but you believed the second? Or is your conclusion making sense of both?